1
|
Masuku K, Menéndez-Méndez LM, Noki S, de la Torre BG, Albericio F, Fernández S, Ferrero M, Aviñó A, Eritja R, Fàbrega C. The synthesis of solid supports carrying base labile linkers to generate 3'-phosphate oligonucleotides. Bioorg Med Chem Lett 2024; 109:129819. [PMID: 38810710 DOI: 10.1016/j.bmcl.2024.129819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
Oligonucleotides carrying 3'-terminal phosphates and conjugates are important tools in molecular biology and diagnostic purposes. We described the preparation of solid supports carrying the base labile linker 4-((2-hydroxyethyl)sulfonyl)benzamide for the solid-phase synthesis of 3'-phosphorylated oligonucleotides. These supports are fully compatible with the phosphoramidite chemistry yielding the desired 3'-phosphate oligonucleotides in excellent yields. The use of mild deprotection conditions allows the generation of partially protected DNA fragments.
Collapse
Affiliation(s)
- Kwazi Masuku
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Luis Miguel Menéndez-Méndez
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain; Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Química Organometálica "Enrique Moles", Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
| | - Sikabwe Noki
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Beatriz G de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa; CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; Department of Organic Chemistry, University of Barcelona, Martí I Franques 1-11, 08028 Barcelona, Spain
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa; CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain; Department of Organic Chemistry, University of Barcelona, Martí I Franques 1-11, 08028 Barcelona, Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Química Organometálica "Enrique Moles", Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Química Organometálica "Enrique Moles", Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
| | - Anna Aviñó
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Carme Fàbrega
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain; IQAC-CSIC. Jordi Girona 18-26, 08034 Barcelona, Spain.
| |
Collapse
|
2
|
Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
Collapse
Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| |
Collapse
|
3
|
Saraya JS, O'Flaherty DK. A Facile and General Tandem Oligonucleotide Synthesis Methodology for DNA and RNA. Chembiochem 2024; 25:e202300870. [PMID: 38179859 DOI: 10.1002/cbic.202300870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/06/2024]
Abstract
Tandem oligonucleotide synthesis (TOS) is an attractive strategy to increase automated oligonucleotide synthesis efficiency. TOS is accomplished via the introduction of an immolative linker within a single sequence composed of multiple oligonucleotide fragments. Here, we report the use of a commercially available building block, typically utilized for the chemical phosphorylation of DNA/RNA oligomers, to perform TOS. We show that the 2,2'-sulfonyldiethylene linker is efficiently self-immolated during the standard deprotection of DNA and RNA and presents itself as a generalizable methodology for nucleic acid TOS. Furthermore, we show the utility of this methodology by assembling a model siRNA construct, and showcase a template-directed ligation pathway to incorporate phosphoramidate or pyrophosphate linkages within DNA oligomers.
Collapse
Affiliation(s)
- Jagandeep S Saraya
- Department of Chemistry, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada)
| | - Derek K O'Flaherty
- Department of Chemistry, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada)
| |
Collapse
|
4
|
Krygier D, Przybyła M, Chmielewski MK. Microwave-Dependent Thermo-Release Approach for Oligonucleotides 5'-Phosphorylation. Org Lett 2024; 26:1134-1137. [PMID: 38307039 DOI: 10.1021/acs.orglett.3c03924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
A method for phosphorylating oligonucleotides using a thermosensitive "trigger" is hereby presented. The recovery of the phosphate specifically takes place under neutral conditions when subjected to an elevated temperature. Two identical thermolabile protecting groups are differentially removed with the initial release occurring swiftly and the second at a more gradual pace. The delayed deprotection of the second group led to the development of a method for the purification of 5'-phosphorylated oligonucleotides. Microwave irradiation enables the rapid attainment of complete deprotection, in contrast to conventional heating methods.
Collapse
Affiliation(s)
- Dominika Krygier
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Mikołaj Przybyła
- FutureSynthesis sp. z o.o., ul. Rubież 46B, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
- BioSynthesis sp. z o.o., ul. Rubież 46H/229, 61-612 Poznań, Poland
| |
Collapse
|
5
|
Madaoui M, Meyer A, Vasseur JJ, Morvan F. Thermolytic Reagents to Synthesize 5′- or 3′-Mono(thio)phosphate Oligodeoxynucleotides or 3′-modified oligodeoxynucleotides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mimouna Madaoui
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - François Morvan
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| |
Collapse
|
6
|
Pradère U, Halloy F, Hall J. Chemical synthesis of long RNAs with terminal 5'-phosphate groups. Chemistry 2017; 23:5210-5213. [PMID: 28295757 PMCID: PMC5413853 DOI: 10.1002/chem.201700514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Long structured RNAs are useful biochemical and biological tools. They are usually prepared enzymatically, but this precludes their site-specific modification with functional groups for chemical biology studies. One solution is to perform solid-phase synthesis of multiple RNAs loaded with 5'-terminal phosphate groups, so that RNAs can be concatenated using template ligation reactions. However, there are currently no readily available reagents suitable for the incorporation of the phosphate group into long RNAs by solid-phase synthesis. Here we describe an easy-to-prepare phosphoramidite reagent suitable for the chemical introduction of 5'-terminal phosphate groups into long RNAs. The phosphate is protected by a dinitrobenzhydryl group that serves as an essential lipophilic group for the separation of oligonucleotide by-products. The phosphate is unmasked quantitatively by brief UV irradiation. We demonstrate the value of this reagent in the preparation of a library of long structured RNAs that are site-specifically modified with functional groups.
Collapse
Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| | - François Halloy
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| | - Jonathan Hall
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| |
Collapse
|
7
|
Romanucci V, Zarrelli A, Guaragna A, Di Marino C, Di Fabio G. New phosphorylating reagents for deoxyribonucleosides and oligonucleotides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
8
|
Synthesis and gene silencing properties of siRNAs containing terminal amide linkages. BIOMED RESEARCH INTERNATIONAL 2014; 2014:901617. [PMID: 24791003 PMCID: PMC3984766 DOI: 10.1155/2014/901617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/23/2014] [Indexed: 01/04/2023]
Abstract
The active components of the RNAi are 21 nucleotides long dsRNAs containing a 2 nucleotide overhang at the 3′ end, carrying 5′-phosphate and 3′-hydroxyl groups (siRNAs). Structural analysis revealed that the siRNA is functionally bound at both ends to RISC. Terminal modifications are considered with interest as the introduction of chemical moieties interferes with the 3′ overhang recognition by the PAZ domain and the 5′-phosphate recognition by the MID and PIWI domains of RISC. Herein, we report the synthesis of modified siRNAs containing terminal amide linkages by introducing hydroxyethylglycine PNA (hegPNA) moieties at 5′, and at 3′ positions and on both terminals. Results of gene silencing studies highlight that some of these modifications are compatible with the RNAi machinery and markedly increase the resistance to serum-derived nucleases even after 24 h of incubation. Molecular docking simulations were attained to give at atomistic level a clearer picture of the effect of the most performing modifications on the interactions with the human Argonaute 2 PAZ, MID, and PIWI domains. This study adds another piece to the puzzle of the heterogeneous chemical modifications that can be attained to enhance the silencing efficiency of siRNAs.
Collapse
|
9
|
Su M, Wang J, Tang X. Photocaging strategy for functionalisation of oligonucleotides and its applications for oligonucleotide labelling and cyclisation. Chemistry 2012; 18:9628-37. [PMID: 22767502 DOI: 10.1002/chem.201103833] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 05/14/2012] [Indexed: 12/15/2022]
Abstract
We have used a photocaging strategy to develop novel phosphoramidites and expand the repertoire of protecting groups for modification of oligonucleotides by solid-phase synthesis. We synthesised five photolabile phosphoramidites and four new photolabile controlled pore glasses (CPGs). By using these photolabile phosphoramidites and CPGs, modified oligodeoxynucleotides (ODNs) with phosphate, amine, acid, thiol and carbonyl moieties at 5' and/or 3' ends were readily synthesised. To the best of our knowledge, this is the first report of introducing a carbonyl at the 5' end and thiol groups at both ends of ODNs with photolabile modifiers. Terminal labelling was also easily realised in solution or by on-column solid-phase synthesis. By using the photolabile amine modifier and the photolabile acid CPG, cyclisation of an oligodeoxynucleotide was achieved with good yields. This study provides an alternative way to introduce functional groups into oligonucleotides and expand the scope of oligonucleotide bio-orthogonal labelling.
Collapse
Affiliation(s)
- Meng Su
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing 100191, P. R. China
| | | | | |
Collapse
|
10
|
Sallamand C, Miscioscia A, Lartia R, Defrancq E. Phosphorylating reagent-free synthesis of 5'-phosphate oligonucleotides by controlled oxidative degradation of their 5'-end. Org Lett 2012; 14:2030-3. [PMID: 22480332 DOI: 10.1021/ol300542s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5'-phosphorylated oligonucleotides (5'-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5'-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5'-nucleoside and subsequent formation of the 5'-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.
Collapse
Affiliation(s)
- Corinne Sallamand
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
| | | | | | | |
Collapse
|
11
|
Yuan Y, Fueangfung S, Lin X, Pokharel D, Fang S. Synthetic 5′-phosphorylated oligodeoxynucleotide purification through catching full-length sequences by polymerization. RSC Adv 2012. [DOI: 10.1039/c2ra01357f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
|
12
|
Paredes E, Evans M, Das SR. RNA labeling, conjugation and ligation. Methods 2011; 54:251-9. [PMID: 21354310 DOI: 10.1016/j.ymeth.2011.02.008] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 01/19/2023] Open
Abstract
Advances in RNA nanotechnology will depend on the ability to manipulate, probe the structure and engineer the function of RNA with high precision. This article reviews current abilities to incorporate site-specific labels or to conjugate other useful molecules to RNA either directly or indirectly through post-synthetic labeling methodologies that have enabled a broader understanding of RNA structure and function. Readily applicable modifications to RNA can range from isotopic labels and fluorescent or other molecular probes to protein, lipid, glycoside or nucleic acid conjugates that can be introduced using combinations of synthetic chemistry, enzymatic incorporation and various conjugation chemistries. These labels, conjugations and ligations to RNA are quintessential for further investigation and applications of RNA as they enable the visualization, structural elucidation, localization, and biodistribution of modified RNA.
Collapse
Affiliation(s)
- Eduardo Paredes
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | | |
Collapse
|
13
|
Ovaere M, Van Aerschot A, Abramov M, Herdewijn P, Van Meervelt L. Crystallization and preliminary X-ray study of the D-altritol oligonucleotide GTGTACAC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:460-2. [PMID: 20383022 PMCID: PMC2852344 DOI: 10.1107/s1744309110007050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 02/24/2010] [Indexed: 11/10/2022]
Abstract
In altritol nucleic acids (ANAs), the natural five-membered ribose ring of RNA is replaced by the six-membered D-altritol ring. ANAs are good candidates to act as siRNAs in the RNA-interference pathway. Crystals of the fully modified altritol self-complementary octamer GTGTACAC were grown by the hanging-drop vapour-diffusion technique at 289 K. Diffraction data were recorded on SLS beamline X06DA and processed to 3.0 A resolution. The crystals belonged to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = 25.05, c = 117.58 A.
Collapse
Affiliation(s)
- Margriet Ovaere
- Department of Chemistry, Biomolecular Architecture and BioMacS, Katholieke Universiteit Leuven, Belgium
| | - Arthur Van Aerschot
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research and BioMacS, Katholieke Universiteit Leuven, Belgium
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research and BioMacS, Katholieke Universiteit Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research and BioMacS, Katholieke Universiteit Leuven, Belgium
| | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture and BioMacS, Katholieke Universiteit Leuven, Belgium
| |
Collapse
|
14
|
Nilsson M, Landegren U, Antson DO. Single-nucleotide sequence discrimination in situ using padlock probes. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.8. [PMID: 18770746 DOI: 10.1002/0471142956.cy0808s16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Standard fluorescence in situ hybridization (FISH) techniques using cloned probes are limited in their ability to distinguish between closely similar DNA sequences because long hybridization probes are not detectably destabilized by single mismatched base pairs. This problem has been addressed by using short allele-specific oligonucleotide probes whose hybridization to target sequences is more sensitive to mismatches. This revised and expanded unit presents protocols for discrimination between closely similar DNA sequences in situ. The discussion of probe synthesis has been greatly expanded and an Alternate Protocol 1 added for enzymatic probe ligation at low probe concentration. A new Support Protocol describes enzymatic probe synthesis.
Collapse
|
15
|
Fang S, Bergstrom DE. Reversible biotinylation of the 5'-terminus of oligodeoxyribonucleotides and its application in affinity purification. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.20. [PMID: 18428910 DOI: 10.1002/0471142700.nc0420s14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The preparation of two reversible biotinylation phosphoramidites and their application in labeling and affinity purification of synthetic oligodeoxyribonucleotides will be described. In both cases, the biotin is linked to the 5'-terminus of DNA through a diisopropyl silyl acetal functionality. This linkage is completely stable under certain postsynthetic cleavage/deprotection conditions, but can be readily broken by fluoride ions, releasing unmodified 5'-OH and 5'-phosphate DNA, respectively. To demonstrate the use of these reversible biotinylation methods, crude DNA was incubated with NeutrAvidin-coated microspheres, full-length biotinylated DNA was efficiently attached to the solid phase, and nonbiotinylated failure sequences and other impurities were readily removed by washing with buffer. Cleavage of the silyl acetal linkage afforded high-quality, full-length, unmodified 5'-OH and 5'-phosphate DNA, respectively, depending on which of the two phosphoramidites was used. It is anticipated that this method will find applications in areas that require efficient isolation of DNA from a complex mixture.
Collapse
Affiliation(s)
- Shiyue Fang
- Purdue University, West Lafayette, Indiana, USA
| | | |
Collapse
|
16
|
Thuong NT, Asseline U. Modification of the 5' terminus of oligonucleotides for attachment of reporter and conjugate groups. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.2. [PMID: 18428849 DOI: 10.1002/0471142700.nc0402s00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Reporter and conjugate groups can be added directly to the 5' terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5' modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step-by-step protocols for attachment of conjugate groups are given elsewhere in the series.
Collapse
Affiliation(s)
- N T Thuong
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | | |
Collapse
|
17
|
Seliger H. Protection of 5'-hydroxy functions of nucleosides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2008; Chapter 2:Unit 2.3. [PMID: 18428836 DOI: 10.1002/0471142700.nc0203s00] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The 5-hydroxy group is the primary hydroxy group of nucleosides. It is mandatory to protect 5-hydroxyls in all methods of oligonucleotide synthesis that require nucleoside synthons. This unit discusses a wide variety of acid-labile and base-labile protecting groups, as well as enzymatic methods for 5-protection and deprotection.
Collapse
|
18
|
Tabatadze D, Zamecnik P, Yanachkov I, Wright G, Pierson K, Zhang S, Bogdanov A, Metelev V. A novel thymidine phosphoramidite synthon for incorporation of internucleoside phosphate linkers during automated oligodeoxynucleotide synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:157-72. [PMID: 18205070 DOI: 10.1080/15257770701795938] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A novel thymidine phosphoramidite synthon was synthesized and successfully used for incorporation of primary amino groups, attached through a triethylene glycol linker to the internucleoside phosphates, at desired locations during automated oligodeoxynucleotide synthesis. The synthesized amino-linker bearing oligonucleotides are stable under deprotection conditions and exhibit Watson-Crick base-pairing properties. Covalent labeling of oligonucleotides with carbocyanine near-infrared fluorochromes resulted in 2.5 times higher labeling yields when compared with oligonucleotides containing base-attached aminolinkers. We anticipate that the developed synthetic approach will be useful for nucleotide sequence-specific attachment of single or multiple ligands or reporter molecules.
Collapse
Affiliation(s)
- David Tabatadze
- Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Lewdorowicz M, Jemielity J, Kierzek R, Shapira M, Stepinski J, Darzynkiewicz E. Solid-supported synthesis of 5'-mRNA CAP-4 from Trypanosomatids. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1329-33. [PMID: 18066778 DOI: 10.1080/15257770701533065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The unique structure of 5' mRNA cap from Trypanosomatids is the most modified cap found in nature. Here we present the synthesis of cap-4 (m(7)Gpppm(3)(6,6,2')Apm(2')Apm(2')Cpm(2)(3,2')Up) on a disulfide-tethered solid support. This approach allows obtaining cap-4 more efficiently then previously described. Moreover such modified resin could be a useful tool for affinity purification of Leishmania proteins interacting with cap-4. For the final step of synthesis, namely coupling of phosphorylated tetranucleotide with activated 7-methylguanosine 5'-diphosphate two systems were compared. Surprisingly, the coupling in water with Mn(2+) as a catalyst, gave better results than usually more effective coupling in DMF with ZnCl(2).
Collapse
Affiliation(s)
- Magdalena Lewdorowicz
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, Zwirki i Wigury 93, Warsaw 02-089, Poland
| | | | | | | | | | | |
Collapse
|
20
|
Paranjape JM, Xu D, Kushner DM, Okicki J, Lindner DJ, Cramer H, Silverman RH, Leaman DW. Human telomerase RNA degradation by 2'-5'-linked oligoadenylate antisense chimeras in a cell-free system, cultured tumor cells, and murine xenograft models. Oligonucleotides 2006; 16:225-38. [PMID: 16978086 DOI: 10.1089/oli.2006.16.225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ribonuclease L (RNase L) is a latent single-stranded RNA-directed endoribonuclease that is activated on binding to short 2'-5'-linked oligoadenylates (2-5A), a feature that has led to its use in antisense therapeutic strategies. By attaching a 2-5A moiety to the 5' terminus of standard antisense oligonucleotides, it is possible to activate RNase L and guide it to specific RNAs for degradation. These 2-5A antisense chimeras have been used successfully to target a variety of cellular and viral RNAs. Telomerase is a nuclear ribonucleoprotein complex that elongates telomeric DNA and contributes to cellular immortalization. Telomerase is composed of a protein catalytic subunit and an RNA (hTR or TERC) component, both of which are critical for holoenzyme activity. We describe the characterization of 2-5A antisense chimeras targeting the hTR component of telomerase (2-5A antihTR). Newly designed 2-5A anti-hTR molecules were assayed for their abilities to selectively degrade hTR in a cell-free system. Of the five chimeras tested, one (RBI011) degraded hTR by 97%, and two others (RBI013 and RBI009) were also found to be highly active (73-76% degradation). The ability of transfected RBI011, and its homolog RBI254, to degrade hTR in cultured tumor cells was assessed by real-time RT-PCR. In these studies, RBI011 and RBI254 effectively degraded hTR in a variety of hTR-positive tumor cell lines. The hTR degradation studies were extended to growth assays to determine whether hTR ablation affected tumor cell viability or proliferation. RBI254 treatment resulted in reduced tumor cell viability over the course of 4-day growth assays, effects that were augmented by cotreatment with interferon-beta. To extend these results to an in vivo system, nude mice were implanted subcutaneously or orthotopically with hTR-positive prostate tumors and treated with RBI254. RBI254-treated mice exhibited enhanced tumor cell apoptosis and reduced tumor volume as compared with controls. These findings demonstrated the effectiveness of highly active forms of 2-5A antisense against hTR, and also highlight the usefulness of the cell-free system in predicting chimera efficacy before to inception of cell-based and in vivo studies.
Collapse
Affiliation(s)
- Jayashree M Paranjape
- Department of Cancer Biology and Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Meyer A, Bouillon C, Vidal S, Vasseur JJ, Morvan F. A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Ausín C, Grajkowski A, Cieślak J, Beaucage SL. Chemical phosphorylation of deoxyribonucleosides and thermolytic DNA oligonucleotides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2006; Chapter 13:Unit 13.6. [PMID: 18428949 DOI: 10.1002/0471142700.nc1306s26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The phosphorylating reagent bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite is prepared in three steps from commercial methyl thioglycolate and diisopropylphosphoramidous dichloride. The phosphorylating reagent has been used successfully in the solid-phase synthesis of deoxyribonucleoside 5'-/3'-phosphate or -thiophosphate monoesters and oligonucleotide 5'-phosphate/-thiophosphate monoesters. Bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite has also been employed in the construction of a thermolytic dinucleotide prodrug model to evaluate the ability of the reagent to produce thermosentive oligonucleotide prodrugs under mild temperature conditions ( approximately 25 degrees C) for potential therapeutic applications.
Collapse
Affiliation(s)
- Cristina Ausín
- Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
| | | | | | | |
Collapse
|
23
|
Ausín C, Grajkowski A, Cieślak J, Beaucage SL. An efficient reagent for the phosphorylation of deoxyribonucleosides, DNA oligonucleotides, and their thermolytic analogues. Org Lett 2006; 7:4201-4. [PMID: 16146387 DOI: 10.1021/ol0516263] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The phosphoramidite 11 was prepared in three steps from methyl 2-mercaptoacetate and demonstrated efficiency in the synthesis of conventional 5'-/3'-phosphate/thiophosphate monoester derivatives of 2'-deoxyribonucleosides and DNA oligonucleotides. Moreover, the use of 11 has enabled the preparation of the dinucleoside phosphorothioate analogue 26 in high yields (>95%) with minimal cleavage (<2%) of the thermolytic thiophosphate protecting group.
Collapse
Affiliation(s)
- Cristina Ausín
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
| | | | | | | |
Collapse
|
24
|
Jemielity J, Heinonen P, Lonnberg H, Darzynkiewicz E. A novel approach to solid phase chemical synthesis of oligonucleotide mRNA cap analogs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:601-5. [PMID: 16247996 DOI: 10.1081/ncn-200061922] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A novel approach for the synthesis of 5-capped 2'-O-methyloligoribonucleotides on a disulfide-tethered solid support is described. The key step of the synthesis is ZnCl2 promoted coupling of m7GDP imidazolide to a fully deprotected oligonucleotide 5'-phosphate on-support. By this methodology m7G5'pppm2'Apm2'Upm2'Ap has been prepared.
Collapse
Affiliation(s)
- Jacek Jemielity
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, Zwirki i Wigury 93, Warsaw 0289, Poland.
| | | | | | | |
Collapse
|
25
|
New phosphoramidite derivatives for the preparation of oligonucleotides containing a hydrazide group in any specified position of the oligonucleotide chain. Russ Chem Bull 2005. [DOI: 10.1007/s11172-006-0175-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Lewdorowicz M, Yoffe Y, Zuberek J, Jemielity J, Stepinski J, Kierzek R, Stolarski R, Shapira M, Darzynkiewicz E. Chemical synthesis and binding activity of the trypanosomatid cap-4 structure. RNA (NEW YORK, N.Y.) 2004; 10:1469-78. [PMID: 15273325 PMCID: PMC1370633 DOI: 10.1261/rna.7510504] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Leishmania and other trypanosomatids are early eukaryotes that possess unusual molecular features, including polycistronic transcription and trans-splicing of pre-mRNAs. The spliced leader RNA (SL RNA) is joined to the 5' end of all mRNAs, thus donating a 5' cap that is characterized by complex modifications. In addition to the conserved m7GTP, linked via a 5'-5'-triphosphate bound to the first nucleoside of the mRNA, the trypanosomatid 5' cap includes 2'-O methylations on the first four ribose moieties and unique base methylations on the first adenine and the fourth uracil, resulting in the cap-4 structure, m7Gpppm3(6,6,2')Apm2'Apm2' Cpm2(3,2')U, as reported elsewhere previously. A library of analogs that mimic the cap structure to different degrees has been synthesized. Their differential affinities to the cap binding proteins make them attractive compounds for studying the molecular basis of cap recognition, and in turn, they may have potential therapeutic significance. The interactions between cap analogs and eIF4E, a cap-binding protein that plays a key role in initiation of translation, can be monitored by measuring intrinsic fluorescence quenching of the tryptophan residues. In the present communication we describe the multistep synthesis of the trypanosomatid cap-4 structure. The 5' terminal mRNA tetranucleotide fragment (pm3(6,6,2')Apm2'Apm2'Cpm2(3,2')U) was synthesized by the phosphoramidite solid phase method. After deprotection and purification, the 5'-phosphorylated tetranucleotide was chemically coupled with m7GDP to yield the cap-4 structure. Biological activity of this newly synthesized compound was confirmed in binding studies with eIF4E from Leishmania that we recently cloned (LeishIF4E-1), using the fluorescence time-synchronized titration method.
Collapse
Affiliation(s)
- Magdalena Lewdorowicz
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, 93 Zwirki and Wigury St., 02-089, Poland
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Lartia R, Asseline U. New reagent for the preparation of oligonucleotides involving a 5′-thiophosphate or a 5′-phosphate group. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
28
|
|
29
|
Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
30
|
Nilsson M, Landegren U, Antson DO. Single-nucleotide sequence discrimination in situ using padlock probes. CURRENT PROTOCOLS IN HUMAN GENETICS 2002; Chapter 4:Unit 4.11. [PMID: 18428329 DOI: 10.1002/0471142905.hg0411s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA ligases are very sensitive to mismatches at the DNA ends to be joined through ligation. This mechanism has been exploited to distinguish DNA sequence variants in situ using so-called padlock probes. Padlock probes are linear oligonucleotides with target-complementary sequences at both ends, and an on-target-complementary segment in between. The end sequences are brought next to each other upon hybridization to the target DNA sequence, and if the ends are perfectly matched to the target sequence, they can be joined by a DNA ligase. Padlock probes detect target sequences with very high specificity, because both probe segments must hybridize to the target for circularization to occur. This unit presents a protocol for discrimination between closely similar DNA sequences in situ using padlock probes. A discussion of methods for greatly amplifying the signal from circularized probes is also included.DNA ligases are very sensitive to mismatches at the DNA ends to be joined through ligation.
Collapse
|
31
|
Guzaev AP, Manoharan M. Novel reagents for terminal phosphorylation and thiophosphorylation of synthetic oligonucleotides. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00834-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
32
|
The 3rd Annual NIH Symposium on Therapeutic Oligonucleotides. Bethesda, Maryland, USA. December 4, 1998. Abstracts. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:359-431. [PMID: 10498436 DOI: 10.1089/oli.1.1999.9.359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
33
|
|
34
|
Guzaev A, Lönnberg H. A novel solid support for synthesis of 3′-phosphorylated chimeric oligonucleotides containing internucleosidic methyl phosphotriester and methylphosphonate linkages. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00739-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
35
|
|